Response to Bean et al. (2018): Gain‐of‐function mutations in beet DODA2 identify key residues for betalain pigment evolution

Code in this repository is provided as-is and comes with absolutely no warranty. Feel free to share and use (at your own risk) but cite the paper when you do.

Contents

• phylogenetics
  • data
    • alignment.pep.fa.clustalo.aln: clustalo alignment of amino acid sequences
    • alignment.pep.fa.clustalo.aln-cln: clustalo alignment of amino acid sequences, only >= 95% occupancy columns
    • alignment.pep.fa.clustalo.aln-cln.treefile: inferred tree, with 200 non-parametric bootstrap replicates
    • alignment_BvDODAa2_corres.tsv: correspondence between cleaned alignment positions and sites in BvDODAa2
    • DODA1_DODA2_jsd.csv: Jensen-Shannon Divergences between DODA1- and DODA2-like sequences in the cleaned alignment
    • sequences.cds.fa: coding sequences included in analysis
    • sequences.pep.fa: amino acid sequences included in analysis
  • scripts
    • calc_site_specific_divergence_aa.py: script to calculate site-specific amino acid divergences
    • color_resi_pymol.py: a PyMOL function to colour multiple residues based on values in a table
    • DODA1_DODA2_colours_for_pymol.R: script to get colours for PyMOL
    • parse_fasta.py: utility
• statistics
  • data
    • Nbenthamiana_MN.csv: CSV to reproduce Fig 4a
    • Scerevisiae_GI.csv: CSV to reproduce Fig 4b
    • Scerevisiae_HC.csv: CSV to reproduce Fig 4c
    • DODA_activity_diff_pH.csv: CSV to reproduce Fig 5a
    • DODAa2_a2-mut3_activity_pH8.5.csv: CSV to reproduce Fig 5b
    • DODA_activity_pH6.csv: CSV to reproduce Fig 5c
  • scripts
    • analysis.R: R script for statistical analysis
    • curve_fitting.R: R script for enzymatic analysis